Hi,
I keep running into this error and I have no idea what to do about it. I’ve tried 3 different versions of mothur (1.31, 1.33, and 1.34) with the same result.
[ERROR]: HWI-M02808_51_A9K3P_1_1102_6529_19859 is in your groupfile and not your listfile. Please correct.
[ERROR]: HWI-M02808_51_A9K3P_1_2107_16825_10620 is in your groupfile and not your listfile. Please correct.
[ERROR]: HWI-M02808_51_A9K3P_1_2107_17397_16544 is in your groupfile and not your listfile. Please correct.
[ERROR]: HWI-M02808_51_A9K3P_1_2112_5166_10436 is in your groupfile and not your listfile. Please correct.
Your group file contains 136663 sequences and list file contains 136659 sequences. Please correct.
The error occurs when I run the make.shared command:
make.shared(list=quality_sequences.an.unique_list.list, count=quality_sequences.count_table, label=0.03)
The commands that I ran prior to this step are as follows:
make.contigs(file=cecal_transfer.files, processors=8)
screen.seqs(fasta=cecal_transfer.trim.contigs.fasta, group=cecal_transfer.contigs.groups, maxambig=0, maxlength=275)
unique.seqs(fasta=current)
count.seqs(name=current, group=current)
pcr.seqs(fasta=silva.bacteria.fasta, start=11894, end=25319, keepdots=F, processors=8)
system(mv silva.bacteria.pcr.fasta silva.v4.fasta)
align.seqs(fasta=cecal_transfer.trim.contigs.good.unique.fasta, reference=silva.v4.fasta)
screen.seqs(fasta=current, count=current, summary=current, start=1968, end=11550, maxhomop=8)
filter.seqs(fasta=cecal_transfer.trim.contigs.good.unique.good.align, vertical=T, trump=.)
unique.seqs(fasta=current, count=current)
pre.cluster(fasta=current, count=current, diffs=2)
chimera.uchime(fasta=current, count=current, dereplicate=t)
remove.seqs(fasta=current, accnos=current)
classify.seqs(fasta=current, count=current, reference=trainset9_032012.pds.fasta, taxonomy=trainset9_032012.pds.tax, cutoff=80)
remove.lineage(fasta=current, count=current, taxonomy=current, taxon=Chloroplast-Mitochondria-unknown-Archaea-Eukaryota)
cp cecal_transfer.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta quality_sequences.fasta
cp cecal_transfer.trim.contigs.good.unique.good.filter.unique.precluster.uchime.pick.pick.count_table quality_sequences.count_table quality_sequences.count_table
cp cecal_transfer.trim.contigs.good.unique.good.filter.unique.precluster.pick.pds.wang.pick.taxonomy quality_sequences.taxonomy
cp cecal_transfer.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.pick.an.unique_list.list quality_sequences.an.unique_list.list
set.current(fasta=quality_sequences.fasta, count=quality_sequences.count_table, taxonomy=quality_sequences.taxonomy, processors=8)
dist.seqs(fasta=current, cutoff=0.2)
cluster.split(column=current, count=current, taxonomy=current, splitmethod=classify, taxlevel=4, cutoff=0.15)